Recurrent selection and reduction in recombination shape the genomic landscape of divergence across multiple population pairs of Green-backed Tit

Lay SummaryDisentangling evolutionary forces that drive genomic divergence is necessary for advancing our understanding of speciation. Previous studies have compared genomic landscapes of divergence across different populations and species. Here we present a genomic divergence at multiple stages of lineage divergence in the Green-backed tit (Parus monticolus). We found that the lineages that have diverged at different stages differ in the degree to which they display genomic peaks of divergence and in the location of these peaks. The lineages that split a long time ago tend to have fewer but more corresponding genomic islands than the lineages that have split more recently. Recurrent selection in regions with low recombination is the major driver of genomic divergence. The highly differentiated genomic regions under the target of selection are more likely resist to genetic introgression. Overall, this study shows that the combination of common ancestry, recurrent selection, low recombination, and gene flow has shaped genomic divergence at different stages across the speciation.